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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $species_info = array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ) $local_species = 'bvu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $species_info = array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ) $local_species = 'esa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $species_info = array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ) $local_species = 'sgi' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ), 'gf_id' => 'HOM05D001516', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001516' ), 'data_identifier' => 'HOM05D001516', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001516', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '418', 'num_species' => '97' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03040' => 'bna', 'A02p11350' => 'bna', 'A02p19380' => 'bna', 'A07p16930' => 'bna', 'A07p40290' => 'bna', 'A08p30210' => 'bna', 'A10p10520' => 'bna', 'Aa31LG1G15540' => 'aar', 'Aa31LG3G11140' => 'aar', 'Aa31LG3G9440' => 'aar', 'Aa31LG4G4740' => 'aar', 'Aa31LG6G12560' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_362.436' => 'aag', 'Actinidia04889' => 'ach', 'Actinidia08658' => 'ach', 'Actinidia34228' => 'ach', 'Ah.02g113540' => 'amhyb', 'Ah.07g205510' => 'amhyb', 'Ah.13g070380' => 'amhyb', 'AL1031U10020' => 'aly', 'AL1G31300' => 'aly', 'AL2G23160' => 'aly', 'AL2G34360' => 'aly', 'AL7G15560' => 'aly', 'AL8G27660' => 'aly', 'AL8G44380' => 'aly', 'Aqoxy2G03603' => 'aox', 'Aqoxy3G03392' => 'aox', 'Aqoxy5G01018' => 'aox', 'Aqoxy6G01631' => 'aox', 'arahy.Tifrunner.gnm1.ann1.632XZS' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.BD7JB4' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.CUW4HR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.DD2ABE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.F3ZCPW' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G1MIMQ' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GWW51V' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ILQ5AU' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.IZ1X2W' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.JXS3UT' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.MYS8SE' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P2WFEB' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8HI4P' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.WBWR58' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.ZR07MJ' => 'arhy', 'AT1G18790' => 'ath', 'AT1G74480' => 'ath', 'AT4G35590' => 'ath', 'AT5G53040' => 'ath', 'AT5G66990' => 'ath', 'ATR0602G211' => 'atr', 'ATR0706G008' => 'atr', 'ATR0807G179' => 'atr', 'Atru.chr3.137' => 'acertr', 'Atru.chr4.1891' => 'acertr', 'AUR62006079' => 'cqu', 'AUR62019415' => 'cqu', 'BcaB03g12956' => 'bca', 'BcaB03g12958' => 'bca', 'BcaB03g12960' => 'bca', 'BcaB05g24855' => 'bca', 'BcaB08g35663' => 'bca', 'BcaC03g15507' => 'bca', 'BcaC04g20514' => 'bca', 'BcaC06g34775' => 'bca', 'BcaC07g38946' => 'bca', 'BcaC08g46880' => 'bca', 'BcaC08g46992' => 'bca', 'BcaC08g46993' => 'bca', 'BcaNung00579' => 'bca', 'BcaNung03642' => 'bca', 'BcaNung03643' => 'bca', 'BolC1t00324H' => 'bol', 'BolC2t08021H' => 'bol', 'BolC2t09223H' => 'bol', 'BolC6t39896H' => 'bol', 'BolC7t42997H' => 'bol', 'BolC8t49517H' => 'bol', 'BolC9t54021H' => 'bol', 'BolC9t57150H' => 'bol', 'BraA01t00286Z' => 'bra', 'BraA02t06198Z' => 'bra', 'BraA02t06977Z' => 'bra', 'BraA07t29419Z' => 'bra', 'BraA07t31572Z' => 'bra', 'BraA08t34954Z' => 'bra', 'BraA10t43136Z' => 'bra', 'C01p03390' => 'bna', 'C02p18760' => 'bna', 'C02p31890' => 'bna', 'C06p48650' => 'bna', 'C07p24760' => 'bna', 'C09p42740' => 'bna', 'CAN.G481.21' => 'can', 'CAN.G837.21' => 'can', 'CANSAT21G0435' => 'cansat', 'CANSAT25G2192' => 'cansat', 'CANSAT80G0145' => 'cansat', 'CARHR019440' => 'chi', 'CARHR067760' => 'chi', 'CARHR128300' => 'chi', 'CARHR243930' => 'chi', 'CARHR266050' => 'chi', 'CARHR280670' => 'chi', 'CARHR280690' => 'chi', 'CARHR287010' => 'chi', 'Carub.0001s1843' => 'cru', 'Carub.0002s2128' => 'cru', 'Carub.0007s0471' => 'cru', 'Carub.0008s1323' => 'cru', 'Carub.0008s2751' => 'cru', 'Ca_05457_v3' => 'car', 'Ca_16717_v3' => 'car', 'Ca_21821_v3' => 'car', 'Ca_24975_v3' => 'car', 'CBR_g4065' => 'cbr', 'CBR_g4618' => 'cbr', 'Cc02_g01410' => 'ccan', 'Cc04_g16590' => 'ccan', 'Cc07_g11770' => 'ccan', 'CDE10G1282' => 'cde', 'Cfa007075' => 'cfa', 'Cfa016240' => 'cfa', 'Cfa018939' => 'cfa', 'Ciclev10027531m.g' => 'ccl', 'CiPaw.06G045400' => 'cil', 'CiPaw.07G003300' => 'cil', 'CiPaw.11G044900' => 'cil', 'CiPaw.12G013100' => 'cil', 'CiPaw.14G103100' => 'cil', 'ClCG01G020910' => 'cla', 'ClCG05G009000' => 'cla', 'COL.COLO4_13416' => 'col', 'COL.COLO4_16774' => 'col', 'COL.COLO4_25381' => 'col', 'Cpa.g.sc3.98' => 'cpa', 'Cpa.g.sc423.7' => 'cpa', 'Cpa.g.sc6.346' => 'cpa', 'Cre01.g000050' => 'cre', 'Cre03.g149350' => 'cre', 'Cre03.g149400' => 'cre', 'Cre03.g153050' => 'cre', 'Cre03.g184600' => 'cre', 'Cre04.g218050' => 'cre', 'Cre06.g297150' => 'cre', 'Cre09.g387850' => 'cre', 'CsaV3_3G019780' => 'csa', 'CsaV3_6G047870' => 'csa', 'CSS0004018' => 'camsi', 'CSS0016781' => 'camsi', 'CSS0019513' => 'camsi', 'CSS0038680' => 'camsi', 'CSS0039932' => 'camsi', 'DCAR_016564' => 'dca', 'DCAR_020327' => 'dca', 'DCAR_020332' => 'dca', 'DCAR_026052' => 'dca', 'DCAR_031992' => 'dca', 'Dinv08169' => 'din', 'Dinv19967' => 'din', 'Dinv29267' => 'din', 'Dinv35343' => 'din', 'Dinv38715' => 'din', 'Dinv40181' => 'din', 'Duzib205G0600' => 'dzi', 'Duzib205G1743' => 'dzi', 'ECA232G3935' => 'eca', 'ECA238G4466' => 'eca', 'ECA246G3832' => 'eca', 'EL10Ac3g05267' => 'bvu', 'EL10Ac5g11022' => 'bvu', 'FAN01G1019' => 'fan', 'FAN02G0369' => 'fan', 'FAN02G1509' => 'fan', 'FAN03G2432' => 'fan', 'FAN04G2572' => 'fan', 'FAN05G1399' => 'fan', 'FAN05G5040' => 'fan', 'FAN06G1894' => 'fan', 'FAN06G2602' => 'fan', 'FAN08G1806' => 'fan', 'FAN09G0040' => 'fan', 'FAN13G2484' => 'fan', 'FAN14G5018' => 'fan', 'FAN18G1478' => 'fan', 'FAN19G0893' => 'fan', 'FAN23G2806' => 'fan', 'FAN26G0778' => 'fan', 'FAN28G1915' => 'fan', 'FvH4_1g10460' => 'fve', 'FvH4_5g14910' => 'fve', 'FvH4_6g10050' => 'fve', 'FvH4_7g31350' => 'fve', 'Glyma.01G159200' => 'gma', 'Glyma.04G169000' => 'gma', 'Glyma.04G234600' => 'gma', 'Glyma.05G026500' => 'gma', 'Glyma.06G129900' => 'gma', 'Glyma.06G130000' => 'gma', 'Glyma.06G194300' => 'gma', 'Glyma.11G085500' => 'gma', 'Glyma.17G100400' => 'gma', 'Gohir.A02G177600' => 'ghi', 'Gohir.A03G051800' => 'ghi', 'Gohir.A09G242400' => 'ghi', 'Gohir.A12G177800' => 'ghi', 'Gohir.D03G002200' => 'ghi', 'Gohir.D03G115300' => 'ghi', 'Gohir.D09G243100' => 'ghi', 'Gohir.D12G180200' => 'ghi', 'Gorai.003G002500' => 'gra', 'Gorai.003G121600' => 'gra', 'Gorai.006G266900' => 'gra', 'Gorai.008G193400' => 'gra', 'GSVIVG01007998001' => 'vvi', 'GSVIVG01026649001' => 'vvi', 'GSVIVG01038562001' => 'vvi', 'HanXRQChr05g0155981' => 'han', 'HanXRQChr09g0258161' => 'han', 'HanXRQChr09g0270851' => 'han', 'Haze_00201' => 'cav', 'Haze_07323' => 'cav', 'Hma1.2p1_0404F.1_g145260' => 'hma', 'Hma1.2p1_1587F.1_g292260' => 'hma', 'Hma1.2p1_1936F.1_g308190' => 'hma', 'Hma1.2p1_2516F.1_g323670' => 'hma', 'Hma1.2p1_2516F.1_g323675' => 'hma', 'HPP92_003653' => 'vpl', 'Lalb_Chr07g0178071' => 'lal', 'Lalb_Chr08g0240161' => 'lal', 'Lalb_Chr09g0321211' => 'lal', 'Lalb_Chr11g0066951' => 'lal', 'Lalb_Chr11g0066961' => 'lal', 'Lalb_Chr13g0303231' => 'lal', 'Lalb_Chr16g0391621' => 'lal', 'Lj1A1018G73' => 'lonja', 'Lj1C1021G15' => 'lonja', 'Lj1g0007070' => 'lja', 'Lj1g0009135' => 'lja', 'Lj1g0012358' => 'lja', 'Lj1g0016444' => 'lja', 'Lj1g0018954' => 'lja', 'Lj1g0026717' => 'lja', 'Lj2A499G36' => 'lonja', 'Lj2g0007675' => 'lja', 'Lj4A234G55' => 'lonja', 'Lj4A234T62' => 'lonja', 'Lj4g0012567' => 'lja', 'Lj5A110G125' => 'lonja', 'Lj9A464G81' => 'lonja', 'Lsat_1_v5_gn_2_63101' => 'lsa', 'Lsat_1_v5_gn_2_73400' => 'lsa', 'Lsat_1_v5_gn_5_19641' => 'lsa', 'Lsat_1_v5_gn_9_49721' => 'lsa', 'Manes.01G184700' => 'mes', 'Manes.02G113900' => 'mes', 'Manes.02G144400' => 'mes', 'Manes.06G092001' => 'mes', 'Manes.14G078300' => 'mes', 'Mapoly0022s0128' => 'mpo', 'MBI02_g15392_MAGBIO' => 'mbi', 'MBI06_g36469_MAGBIO' => 'mbi', 'MBI08_g26556_MAGBIO' => 'mbi', 'MCO05G140' => 'mco', 'MCO06G100' => 'mco', 'MCO13G377' => 'mco', 'MD01G1217600' => 'mdo', 'MD02G1117800' => 'mdo', 'MD06G1193600' => 'mdo', 'MD07G1286800' => 'mdo', 'MD12G1186400' => 'mdo', 'MD14G1200700' => 'mdo', 'MD15G1232500' => 'mdo', 'Medtr0140s0010' => 'mtr', 'Medtr1g069025' => 'mtr', 'Medtr3g091700' => 'mtr', 'Medtr3g091720' => 'mtr', 'Medtr3g435550' => 'mtr', 'Medtr5g024070' => 'mtr', 'MELO3C007974.2' => 'cme', 'MELO3C008502.2' => 'cme', 'MELO3C011670.2' => 'cme', 'MELO3C016458.2' => 'cme', 'MELO3C017174.2' => 'cme', 'Migut.D01815' => 'egut', 'Migut.F01022' => 'egut', 'Migut.I00182' => 'egut', 'Nitab4.5_0000702g0170' => 'nta', 'Nitab4.5_0000702g0190' => 'nta', 'Nitab4.5_0001128g0160' => 'nta', 'Nitab4.5_0005514g0030' => 'nta', 'Nitab4.5_0006000g0120' => 'nta', 'Nitab4.5_0007888g0010' => 'nta', 'Nitab4.5_0011694g0020' => 'nta', 'Nn1g00285' => 'nnu', 'Nn3g18956' => 'nnu', 'Nn4g23180' => 'nnu', 'Nn6g31711' => 'nnu', 'Oeu002100.1' => 'oeu', 'Oeu010694.1' => 'oeu', 'Oeu015920.1' => 'oeu', 'Oeu025701.1' => 'oeu', 'Oeu037181.1' => 'oeu', 'Oeu047294.1' => 'oeu', 'Os04g0564000' => 'osa', 'Os06g0228950' => 'osa', 'Peaxi162Scf00274g00057' => 'pax', 'Peaxi162Scf00740g00141' => 'pax', 'PGR044G0184' => 'pgr', 'PGR083G1206' => 'pgr', 'PGSC0003DMG400018531' => 'stu', 'Phvul.002G116000' => 'pvu', 'Phvul.003G189900' => 'pvu', 'Phvul.009G051600' => 'pvu', 'Phvul.009G186900' => 'pvu', 'Potri.005G101000' => 'ptr', 'Potri.012G016800' => 'ptr', 'Potri.015G011800' => 'ptr', 'Pp3c14_4980' => 'ppa', 'Pp3c15_9360' => 'ppa', 'PRCOL_00003361' => 'pco', 'PRCOL_00007250' => 'pco', 'Prupe.2G308900' => 'ppe', 'Prupe.5G193900' => 'ppe', 'Prupe.7G181600' => 'ppe', 'Psat2g149160' => 'psa', 'Psat3g157600' => 'psa', 'Psat4g050920' => 'psa', 'Psat5g076200' => 'psa', 'Psat5g182200' => 'psa', 'PSO063G5882' => 'pso', 'PSO210G0966' => 'pso', 'PSO541G4990' => 'pso', 'PSO675G7580' => 'pso', 'PSO761G0574' => 'pso', 'PSO832G0026' => 'pso', 'QL06p052912' => 'qlo', 'QL09p002437' => 'qlo', 'QL09p008660' => 'qlo', 'QL10p017048' => 'qlo', 'RcHm_v2.0_Chr1g0380421' => 'rch', 'RcHm_v2.0_Chr2g0097321' => 'rch', 'RcHm_v2.0_Chr3g0460751' => 'rch', 'RcHm_v2.0_Chr7g0181471' => 'rch', 'Rhsim03G0209600' => 'rsi', 'Rhsim08G0154700' => 'rsi', 'Sabra05G0083500' => 'sbr', 'Sabra12G0015600' => 'sbr', 'Sabra15G0009500' => 'sbr', 'SalBow2G3532' => 'sbo', 'SalBow5G5133' => 'sbo', 'Sc04g0002670' => 'sci', 'Sc25g0000920' => 'sci', 'Sed0004547' => 'sed', 'Sed0007845' => 'sed', 'Sed0019456' => 'sed', 'Sed0021767' => 'sed', 'SEGI_20655' => 'sgi', 'SEGI_26765' => 'sgi', 'SEGI_28878' => 'sgi', 'SEGI_29663' => 'sgi', 'SGA_v2.0_scaffold25G10914' => 'sas', 'SGA_v2.0_scaffold55G19777' => 'sas', 'SHI07720' => 'shi', 'SMO114G0017' => 'smo', 'SMO114G0020' => 'smo', 'SMO114G0031' => 'smo', 'SMO114G0034' => 'smo', 'SMO114G0100' => 'smo', 'SMO114G0102' => 'smo', 'SMO114G0111' => 'smo', 'SMO343G0116' => 'smo', 'SMO356G0505' => 'smo', 'Solyc02g005607.1' => 'sly', 'Solyc03g083040.1' => 'sly', 'Solyc03g116010.3' => 'sly', 'Sopen02g001870' => 'spe', 'Sopen03g035000' => 'spe', 'Sp1g16770' => 'spa', 'Sp2g29670' => 'spa', 'Sp5g29660' => 'spa', 'Sp6g15190' => 'spa', 'Sp7g33360' => 'spa', 'TAR376G0518' => 'tar', 'TAR622G1447' => 'tar', 'TAR624G0076' => 'tar', 'TAR628G0852' => 'tar', 'THA.LOC104804550' => 'tha', 'THA.LOC104821259' => 'tha', 'THA.LOC104825152' => 'tha', 'Thecc.01G006000' => 'tca', 'Thecc.03G088400' => 'tca', 'Thecc.03G200500' => 'tca', 'Thhalv10005560m.g' => 'esa', 'Thhalv10009845m.g' => 'esa', 'Thhalv10015321m.g' => 'esa', 'Thhalv10019554m.g' => 'esa', 'Thhalv10027037m.g' => 'esa', 'TPR.G11841' => 'tpr', 'TPR.G18780' => 'tpr', 'TPR.G8366' => 'tpr', 'TPR.G8368' => 'tpr', 'TPR.G8386' => 'tpr', 'TPR.G9267' => 'tpr', 'TWI09G1104' => 'twi', 'TWI39G0641' => 'twi', 'TWI81G1013' => 'twi', 'unitig_0.g2521' => 'ugi', 'unitig_26.g9647' => 'ugi', 'vmacro17540' => 'vma', 'vmacro18462' => 'vma', 'VMungo1215G0517' => 'vmu', 'VMungo1215G1384' => 'vmu', 'VMungo1309G2066' => 'vmu', 'VMungo1309G2746' => 'vmu', 'Zm00001eb073910' => 'zma', 'Zm00001eb254520' => 'zma', 'Zm00001eb372360' => 'zma' ) $gf_id = 'HOM05D001516' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001516' ) $data_identifier = 'HOM05D001516' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 13, 'aar' => (int) 5, 'aag' => (int) 1, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 7, 'aox' => (int) 4, 'arhy' => (int) 15, 'ath' => (int) 5, 'atr' => (int) 3, 'acertr' => (int) 2, 'cqu' => (int) 2, 'bca' => (int) 15, 'bol' => (int) 8, 'bra' => (int) 7, 'can' => (int) 2, 'cansat' => (int) 3, 'chi' => (int) 8, 'cru' => (int) 5, 'car' => (int) 4, 'cbr' => (int) 2, 'ccan' => (int) 3, 'cde' => (int) 1, 'cfa' => (int) 3, 'ccl' => (int) 1, 'cil' => (int) 5, 'cla' => (int) 2, 'col' => (int) 3, 'cpa' => (int) 3, 'cre' => (int) 8, 'csa' => (int) 2, 'camsi' => (int) 5, 'dca' => (int) 5, 'din' => (int) 6, 'dzi' => (int) 2, 'eca' => (int) 3, 'bvu' => (int) 2, 'fan' => (int) 18, 'fve' => (int) 4, 'gma' => (int) 9, 'ghi' => (int) 8, 'gra' => (int) 4, 'vvi' => (int) 3, 'han' => (int) 3, 'cav' => (int) 2, 'hma' => (int) 5, 'vpl' => (int) 1, 'lal' => (int) 7, 'lonja' => (int) 7, 'lja' => (int) 8, 'lsa' => (int) 4, 'mes' => (int) 5, 'mpo' => (int) 1, 'mbi' => (int) 3, 'mco' => (int) 3, 'mdo' => (int) 7, 'mtr' => (int) 6, 'cme' => (int) 5, 'egut' => (int) 3, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 6, 'osa' => (int) 2, 'pax' => (int) 2, 'pgr' => (int) 2, 'stu' => (int) 1, 'pvu' => (int) 4, 'ptr' => (int) 3, 'ppa' => (int) 2, 'pco' => (int) 2, 'ppe' => (int) 3, 'psa' => (int) 5, 'pso' => (int) 6, 'qlo' => (int) 4, 'rch' => (int) 4, 'rsi' => (int) 2, 'sbr' => (int) 3, 'sbo' => (int) 2, 'sci' => (int) 2, 'sed' => (int) 4, 'sgi' => (int) 4, 'sas' => (int) 2, 'shi' => (int) 1, 'smo' => (int) 9, 'sly' => (int) 3, 'spe' => (int) 2, 'spa' => (int) 5, 'tar' => (int) 4, 'tha' => (int) 3, 'tca' => (int) 3, 'esa' => (int) 5, 'tpr' => (int) 6, 'twi' => (int) 3, 'ugi' => (int) 2, 'vma' => (int) 2, 'vmu' => (int) 4, 'zma' => (int) 3 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb372360' $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